S. G. Zhukov

Application of simulated annealing approach for structure solution of molecular crystals from X-ray laboratory powder data

Abstract Simulated annealing approach was successfully applied to solve three unknown molecular structures from X-ray laboratory powder data using a priory known structural fragments. Some possible developments of the method are discussed.

X-ray analysis and computer modeling of the structure of 'relaxor' ferroelectrics Pb3MgNb2O9 and Pb2ScTaO6 in the paraelectric state

A structural study of Pb3MgNb2O9 and ordered Pb2ScTaO6 single crystals is made by X-ray diffraction at high temperatures. Displacements of the Pb atom from the special site are clearly observed. Disordered atomic positions are uniformly distributed over a sphere with radius 0.2–0.3 A and with center at the special position. These atomic displacements are probably caused by local fields due to random statistical distribution of the (Mg, Nb) atoms in Pb3MgNb2O9 and, partially, the (Sc, Ta) atoms in Pb2ScTaO6. Computer modeling, based on the total-energy-minimization method, gives satisfactory agreement with experimental results.

Tris(1-phenacyl-2-pyridone) Hydroxonium Tetrafluoroborate, a Hydrogen-Bonded Complex

The hydrolytic cleavage of 2-phenyloxazolo[3,2-a]pyridinium tetrafluoroborate results in the formation of the title tris(l-phenacyl-2-pyridone) hydroxonium tetrafluoroborate complex, 3C13H11NO2.H3O+.BF4-. The structure is built up from hydrogen-bonded cations and disordered BF4~ anions. The strong hydrogen bonding causes considerable redistribution of electron density in the pyridone moiety.

Heterocyclic Compounds with a Bridge Nitrogen Atom. 14. Cycloaddition of Acetylenedicarboxylic Acid Ester to 2-Chloro-N-phenacylpyridinium Ylide. Crystal Structure of Dimethyl Ester of 5-Chloro-3-(p-nitrobenzoyl)indolizine-1,2-dicarboxylic Acid

Derivative of 5-chloroindolizine is formed in the reaction of 2-chloro-1-(p-nitrophenacyl)pyridinium ylide with acetylenedicarboxylic acid dimethyl ester, the structure of which was demonstrated by X-ray diffraction analysis. According to data of 1H NMR and mass spectra indolizine obtained undergoes an unusual intramolecular cyclization with the formation of benz[e]cycl[3.3.2]azine nucleus.

Structures and tautomeric interconversions of anthraquinone imine derivatives

Substituted 1-hydroxy-9,10-anthraquinone-9-imines have been found to exhibit tautomeric interconversions between the 9,10- and 1,10-quinonoid forms in the solid state as well as in solution. Single-crystal X-ray crystallography was used to study the structures of 4-(N-acetyl-p-tolylamino)-9-amino-1,10-anthracenedione and 4-hydroxy-1-phenylamino-10-mesitylimino-9(10H)-anthracenone at ambient and low temperatures. The former compound gave crystals belonging to the monoclinic space group P2l/c and, at 295 K,a=9.684(2),b=16.371(3),c=12.097(2) å,Β=110.41(1)‡, V=1797 å3,Z=4, R(F)=0.042, and GOF=0.863. The latter compound gave crystals belonging to the monoclinic space group C2/c and, at 295 K,a=38.158(8),b=6.322(2),c=19.325(4) å,Β=101.78(2)‡,V=4564 å3,Z=8, R(F)=0.052, and GOF=0.981, while at 150 K,a=37.852(6),b=6.245(1),c=19.235(4) å,Β=102.81(1)‡,V=4434 å3,R(F)=0.047, and GOF=1.006. Comparison of the geometric parameters of the two compounds illustrates the considerable zwitterionic nature of the first, a distinctive feature of which is a very short bond N(9)-C(9) whose length is essentially equal to that of a double bond. Molecular modeling studies using AMI semiempirical calculations were shown to be capable of satisfactorily reproducing the energetics of the tautomeric equilibrium once the medium effect was taken into account.

THE USE OF CONTINUOUS ATOMIC DISTRIBUTIONS IN STRUCTURAL INVESTIGATIONS

A simple method of describing the scattering from an atom continuously distributed in the unit cell is proposed. Some experimental applications in structural investigations are presented

SOFTWARE AND METHODS FOR PRECISE X-RAY-ANALYSIS

The software package PPXA (programs for precise X-ray analysis) is described, which provides crystallographers with increased precision and reliability of the results of X-ray analysis. The package includes programs for: testing the quality of an automatic four-circle X-ray diffractometer before X-ray experiments; optimization of X-ray diffraction experiments; preliminary processing of experimental data; precise structure analysis up to electron density distribution. The programs for diffractometer testing allow the experimenter to check the stability and precision of the instrument, the homogeneity of the X-ray beam and the detector sensitivity. The programs for preliminary data processing include: corrections for absorption, taking into account the intensity distribution in the X-ray beam cross section; correction or elimination of the simultaneous reflection effect; background subtraction, correcting the effects of the scan-interval cut-off; correction for thermal diffuse scattering (TDS) for crystals in cases of both known and unknown elasticity constants. The programs for precise crystal structure refinement include options for the determination of primary- and secondary-extinction parameters, atomic coordinates, thermal-vibration parameters in harmonic and anharmonic approximations, occupation of atomic positions, atom-core and valence-shell occupation parameters. The programs were written for a MicroVAX-II computer with a VAX/VMS operating system and designed to work with CAD-4 diffractometers and the SDP-Plus software package. A suitable dialogue with a menu system and detailed users instructions are available.

Heterocycles containing a bridge nitrogen atom. 10. Unexpected closure of oxazole ring during the reaction of 2-chloro-1-phenacylpyridinium salt with potassium cyanate. Crystal structure of 2-(p-nitrophenyl)oxazolo-[3,2-a]pyridinium bromide and N-(p-nitrophenacyl)pyrid-2-one

Reaction of 2-chloro-N-(p-nitrophenacyl)pyridinium bromide with potassium cyanate in acetonitrile produces 2-(p-nitrophenyl)oxazolopyridinium bromide. Performing the same reaction in methanol N-(p-nitrophenacyl)pyrid-2-one was isolated. The structures of the obtained products were proved by X-ray structural data.

X-ray mapping in heterocyclic design: II. Diffractometric study of crystalline 2-oxo-2,3-dihydroimidazo[1,2-a]pyridine hydrochloride

The crystal structure of 2-oxo-2,3-dihydroimidazo[1,2-a]pyridine hydrochloride, C7H7ClN2O, is determined by X-ray diffraction. The structure is solved by the direct method and refined by the least-squares procedure to R = 0.0408. The alternation of bond lengths in the molecule is inconsiderable, but does not disappear completely, since no aromatization occurs upon formation of the bicycle from the molecule. This structural change is apparently due to the increased conjugation of the NH group with the pyridine residue of the bicycle. One of the specific structural features of the salt is the formation of the N+-HïCl− hydrogen bond (N-H, 0.792 Å; H⋯Cl, 2.260 Å; and N-H⋯Cl, 171.2°).

Heterocycles with a bridging nitrogen atom. 9. Recyclization of an oxazole fragment to a pyrrole fragment. Synthesis and crystal structure of 5-hexamethylenimino-2-p-nitrophenylindolyzine

X-ray diffraction structural analysis was used to determine the structure of 5-hexamethylenimino-2-p-nitrophenylindolyzine formed in the reaction of 5-methyl-2-p-nitrophenyloxazolo[3,2-a]pyridinium perchlorate with hexamethylenimine.